Agricultural intensification has resulted in a decline of soil biodiversity, and concerns about the deterioration of the biological condition of soils prompted the development of measures to restore soil life. Due to the overwhelming biodiversity of soils, evaluation of such measures is not straightforward, and proxies are used to assess soil health. Because of their trophic diversity, high abundance, and relatively well-characterized ecologies, nematodes are often used as soil health indicators. However, the scarcity of informative morphological characters hampers the upscaling of this proxy. Here we present a community analysis approach that uses nanopore sequencing to generate full-length sequences of small subunit ribosomal DNAs (SSU rDNA). Cover cropping is a common agricultural practice that stimulates soil life, and we mapped the effects of ten cover crop treatments on nematode communities in a field experiment. These analyses included the monitoring of a high impact plant-parasite, Meloidogyne chitwoodi. In total 132 nematode samples were analysed, and 65 nematode taxa were detected, mostly at species level, including representatives of all trophic groups. As a validation, all samples were analysed microscopically for M. chitwoodi, and comparison of count and DNA read data revealed highly similar results. Treatments did not only affect plant-parasitic nematodes, but also free-living nematodes in a cover crop-specific manner. Free-living nematodes from the same trophic group, and even congeneric species, responded differentially to plant-mediated manipulations of the soil microbiome. Hence, nanopore-based SSU rDNA sequencing could facilitate a substantial refinement of the use of nematodes as indicators for soil health.